Structural Bioinformatics Tools for Drug Design
Extraction of Biologically Relevant Information from Structural Databases
Protocol
Channels, tunnels, and pores serve as pathways for the transport of molecules and ions through protein structures, thus participating to their functions. MOLEonline (https://mole.upol.cz
Article
A Correction to this paper has been published: https://doi.org/10.1186/s13321-021-00528-w
Article
Partial atomic charges find many applications in computational chemistry, chemoinformatics, bioinformatics, and nanoscience. Currently, frequently used methods for charge calculation are the Electronegativity ...
Article
Protein structural families are groups of homologous proteins defined by the organization of secondary structure elements (SSEs). Nowadays, many families contain vast numbers of structures, and the SSEs can he...
Article
Plant hormone cytokinins are perceived by a subfamily of sensor histidine kinases (HKs), which via a two-component phosphorelay cascade activate transcriptional responses in the nucleus. Subcellular localizati...
Protocol
LiteMol suite is an innovative solution that enables near-instant delivery of model and experimental biomacromolecular structural data, providing users with an interactive and responsive experience in all mode...
Protocol
Secondary structure elements (SSEs) are inherent parts of protein structures, and their arrangement is characteristic for each protein family. Therefore, annotation of SSEs can facilitate orientation in the va...
Article
Article
Two new TDZ derivatives (HETDZ and 3FMTDZ) are very potent inhibitors of CKX and are promising candidates for in vivo studies.
Book
Extraction of Biologically Relevant Information from Structural Databases
Chapter
This chapter summarizes the purpose and goals of the book.
Chapter
Structural bioinformatics is flourishing from the increased public availability of high-resolution biomacromolecular structures. Careful analysis of these models enables us to study their important structural ...
Chapter
The validation of biomacromolecular structures has become a very important topic, because some published structures have been found to contain serious errors. The presence of ligands is a frequent source of er...
Chapter
Channels are ligand-accessible pathways inside a biomacromolecular structure. These empty voids inside a structure are composed of the surrounding residues, and as such can be viewed as a form of pattern. Impo...
Chapter
Channels are important parts of biomacromolecular structures, because they facilitate the access of ligands to biomacromolecular voids, e.g., active sites, or through a biomacromolecular structure, e.g., trans...
Chapter
Structural bioinformatics offers us a way to benefit from the current enormous volume of biological data and use them to increase our understanding of molecular biology, with further applications in protein en...
Chapter
This chapter introduces tools for the detection and extraction of biomacromolecular fragments (patterns) of interest from biomacromolecular structures. Afterwards, PatternQuery, a query language for the rigoro...
Chapter
provide information about the distribution of electron density within a molecule. Specifically, they reflect the amount of electron density attributed to individual atoms. Information about partial atomic ...
Chapter
This chapter provides two bioinformatics projects, which puts all of the above together in a complete and comprehensible package that provides meaningful biological information. The first project focuses on su...
Chapter
This chapter contains the solutions to the practical exercises, which are focused on work with databases, the validation of structures, detection and extraction of fragments, detection of channels, characteriz...